MasterPATH: network analysis of functional genomics screening data.

Background: Functional genomics employs several experimental approaches to investigate gene functions. High-throughput techniques, such as loss-of-function screening and transcriptome profiling, allow to identify lists of genes potentially involved in biological processes of interest (so called hit list). Several computational methods exist to analyze and interpret such lists, the most widespread of which aim either at investigating of significantly enriched biological processes, or at extracting significantly represented subnetworks.

Identification of microRNAs in skeletal muscle associated with lung cancer cachexia.

Background: Cachexia, highly prevalent in patients with non-small cell lung cancer (NSCLC), impairs quality of life and is associated with reduced tolerance and responsiveness to cancer therapy and decreased survival. MicroRNAs (miRNAs) are small non-coding RNAs that play a central role in post-transcriptional gene regulation. Changes in intramuscular levels of miRNAs have been implicated in muscle wasting conditions.

Mathematical modeling reveals the factors involved in the phenomena of cancer stem cells stabilization.

Cancer Stem Cells (CSC), a subset of cancer cells resembling normal stem cells with self-renewal and asymmetric division capabilities, are present at various but low proportions in many tumors and are thought to be responsible for tumor relapses following conventional cancer therapies. In vitro, most intriguingly, isolated CSCs rapidly regenerate the original population of stem and non-stem cells (non-CSCs) as shown by various investigators. This phenomenon still remains to be explained.

Basic, simple and extendable kinetic model of protein synthesis.

Protein synthesis is one of the most fundamental biological processes. Despite existence of multiple mathematical models of translation, surprisingly, there is no basic and simple chemical kinetic model of this process, derived directly from the detailed kinetic scheme. One of the reasons for this is that the translation process is characterized by indefinite number of states, because of the structure of the polysome.